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June 28, 2014

Trees grow in two ways: they get longer, and they get wider. That doesn’t sound too different from the way an animal grows, but unlike animals, trees only grow longer at their margins. The tip of each stem contains a small cluster of undifferentiated cells called the apical meristem: as these cells divide, the undifferentiated cells are pushed forward and new shoot cells are laid down in their wake. The result? Older cells in a tree’s stem never change position relative to the ground: the part of a 300 foot redwood tree that’s at eye level now was also at eye level when the tree was only 8 feet tall.

So why aren’t trees tall lanky whips of spaghetti-thin twigs? They have another trick, which lets them grow thicker as trunk and branches push out at their tips: the tissues near the outer surface of the stems called secondary meristem. When these tissues divide, they add layers of cells to the outside of the stem, gradually adding girth to the tree, forming rings of new wood over older tissues, and engulfing older branches over time.

Where animals remodel during growth, plants enclose – so every tree contains the shape of its younger self.

June 14, 2014

OK, so I’ve put some alligators through a CT scanner to create three-dimensional models of their cloacas. How exactly is that going to work?

A CT scanner is an ordinary X-ray machine on steroids. The basics for both machines are the same: stick an object-to-be-imaged between an X-ray source and an X-ray detector, and measure the number of X-rays that make it through the object. X-rays are a form of light and do all the same things as ordinary visible wavelengths when they interact with the stuff of the world: some materials bend them, some reflect them, some absorb them. But because X-rays are much more energetic than visible light, more materials are transparent to them. Most visible light bounces off our skin, but to an X-ray it’s as clear as a windowpane.

But an animal’s body isn’t completely transparent to X-rays – molecules in the muscle, fat, and bone can absorb or bend some of the light as it passes through. When this happens, fewer X-rays make it to the detector, and these X-ray-deficient shadows form pictures of the stuff inside the animal.

Your run of the mill X-ray machine takes a picture through a single plane. You’ve no doubt experienced this at the dentist: they stick a detector in your mouth, point a X-ray source at your cheek, and bam! Image of your teeth, roots and all.

CT scanners work on the same principle, but mount the X-ray source and detector in a ring that rotates around the specimen (or person, or whatever) and take many many more pictures in the process. The pictures are fed into a computer program that performs some mathematics I don’t even pretend to understand (this is the “computed tomography” - “CT” - part) and hands back a stack of images that look like a orderly series of planes cut through the specimen. This is a “Z-stack”, and it looks like this:

This particular one (from Julio Pereira) is a stack of images through a human head and chest. Even though the image is in shades of gray, you can clearly see different kinds of tissue: brain, bone, muscle, lungs – all thanks to differences in gray value. Lighter tones represent denser tissues, so bones appear white and the air-filled lungs look black. (Scanning through this particular stack, you can also see a spot where some metal dental work scatters the X-rays into starbursts.)

Importing a Z-stack into specialized image segmentation software makes it possible (again, using some complicated math) to use these grayscale differences to define the surfaces of different tissues throughout the stack and create 3-dimensional models that can be virtually dissected. This fish (scanned and reconstructed by Sarah Faulwetter) is one example: starting with a Z-stack from a CT scan, it's possible to make a model of the surface of the fish that has a model of its skeleton embedded inside it.

June 08, 2014

I don’t teach during the UMass Amherst summer session, but that doesn’t mean I get to spend three months sunbathing in my backyard. As soon as I turn in my final grades, the frenzy of experiments begins – basically everything I don’t have time for during the school year (because I’m, y’know, teaching) gets crammed into the weeks between May and September. This year, I spent the end of May in Louisiana, where I met up with one of my collaborators to work on a 3D anatomical atlas of the alligator cloaca.

Getting ready for his closeup.

This is part of a larger project examining the evolution and function of archosaur reproductive systems: right now, we want to define how the cloacal muscles, blood vessels, and the phallus are oriented relative to one another. And because it's really challenging to define these relationships by dissection alone, we used a modern imaging technique to try to get a more precise picture of the cloaca in situ. In short, we ran 7-foot long American alligators through a CT scanner.

Why so big? We needed mature animals, and alligators don't become sexually mature until they're more than 6 feet long. (These animals were actually on the small side for adult males, but we were also limited by the size of the table in the CT scanner!) So we were lucky to have the expert help of both the wildlife biologists at the Rockefeller Wildlife Refuge and the vets and technicians at the LSU School of Veterinary Medicine for this part of the project. I was amused to see how excited the students were to see what we were doing -- vets-in-training kept stopping by the imaging suite to watch us work.

Of course, collecting the data is just the first step: we’ll be analyzing the images and building 3D computer models for months to come. But it was a particularly thrilling first step.

December 11, 2013

Before there was computed tomography, before there was CLARITY, biologists used clearing and staining to study the three-dimensional anatomy of bones, cartilage, and nerves. The technique is actually straightforward, if time-consuming: soak a whole animal (dead, of course) in materials that make its skin and muscles transparent, while applying stains that meld to specific kinds of tissue.

The results are gorgeous.

A skeleton in shades of red and blue is revealed through the ghostly outline of the animal. Intricate details that normal dissection can destroy are visible: tiny bones around the eye, miniscule gill supports, the connections in living levers.

These preparations are usually stored in laboratories and the back rooms of museums – they are, after all, made for research - but two museums have brought them (or more precisely, their images) out to the public as art installations.

October 14, 2013

She’s a sweetheart, but like most bird dogs she’s been bred
to be rather – um – inquisitive. And
thanks to that curiosity, last week she wound up looking something like this:

Astra met a porcupine. And it did not want to play with her.

Porcupines are one of the largest rodents living near my
house in New England, second in size only to the beavers that keep themselves
to themselves in the pond down the road. Not that I’ve ever seen a porcupine in
the flesh myself – they’re mostly nocturnal, and I don’t go stumbling around
our woods at night. But at this time of year, the porcupines are out looking
for love. Searching for potential mates in the crisp fall air leaves them awake
and active at odd hours, raising the chance that they’ll run into a potential
predator (or an exuberant housepet).

Fortunately for them, porcupines have a phenomenal defense
mechanism. Their backs are covered with quills -- more than 30,000 of them –
long, hollow tubes armed with wicked barbs. One pat with a paw, one playful
nip, and your dog looks like a pincushion.

And pushing back usually means pushing in. The end of a quill doesn’t just have one barb at
its tip: it’s covered with tiny overlapping barbs that point backwards like
rows of wicked teeth. Those barbs tear into skin like a serrated knife blade,
concentrating penetration forces at each tiny point to shred through structural
proteins. It sounds violent, but probably makes a cleaner cut than a smooth
blunt quill could. But it makes the quills something of a challenge to remove.
Pulling a quill backwards spreads out its barbs and anchors them firmly in flesh.
And the barbs’ cutting action means that embedded quills can continue to
migrate through the quilled animal’s body.

Which is why I didn’t take the time for a real photo of my dog plus quills. We were at the vet 10 minutes after her accident. Our vet had them
out in about 15 minutes. And we'll be walking on leash until porcupine mating season is over.

February 17, 2013

There’s really no getting around it – anatomy is a
challenging subject. It’s not just the enormous number of names to memorize.
You also need to remember the relative locations of scores of organs and
muscles and internal spaces and such, which gets even more complicated when you
consider that many of the shapes and spatial relations inside an animal can change when muscles contract. In short, doing 3D
reconstruction in your head on the fly is really hard.

Alligator cloaca, viewed from above (dorsal).

So when I was doing the research for my paper on male
alligator reproductive anatomy, I deliberately dissected the pelvic region of
each of my specimens from a different direction: I worked on one alligator from
the belly upwards, another from its back downwards, and two from the flank
inward. Each direction helped me build a better picture of how muscles wrap
around the cloacal space and where tendons and ligaments thread through the
system and attach to bone. But I still
don’t know what all of those structures look like when the phallus is in its
“functional” position. I think
that some of those muscles squish the cloacal wall into a different shape, but
it’ll take a lot more work, some luck, and really good scientific visualization
methods to find out for sure.

That’s one reason I’m excited about Mieke Roth’scrowdfunding campaign. Her goal? -- to spend a year dissecting Nile crocodile
specimens in John Hutchinson’s lab at the Royal Veterinary College and turning
her drawings and notes into a detailed 3D computer reconstruction of this
magnificent beast. All of it. Head to tail, skin to gut lining. Her fantastic octopus reconstruction is a testament to her
skills, and I for one would love to see her succeed in this larger (much
larger!) endeavor -- and not just because she’ll let me help out when she gets
to the cloaca.